Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: Q16QY

Calculation Name: 2YVS-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2YVS

Chain ID: A

ChEMBL ID:

UniProt ID: Q5SM78

Base Structure: X-ray

Registration Date: 2023-06-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptHSide
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 219
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2544350.248926
FMO2-HF: Nuclear repulsion 2462084.11578
FMO2-HF: Total energy -82266.133146
FMO2-MP2: Total energy -82514.513511


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
ligand interaction
Ligand binding energy
"
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
N/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(A:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
-20.765-14.58323.954-8.431-21.708-0.033
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.025 / q_NPA : -0.011
Distance from base fragment(s) [Å]
Dist
Interaction energy by IFIE and PIEDA
[kcal/mol]
| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >
Fragment charge [e]
FCHARGE q_Mulliken
q_NPA q(I=>J)
Residue
Res #    RES   
Sort
Graph Options
X Axis Label
Y Axis Max Y Axis Min
Display   
frag_NumFragment number. ChainChain species. Res #Residue number. RES3-letter code of amino acid residue, ligand and solvent molecule. FCHARGEFormal charge [e]. q_MullikenFragment charge evaluated by Mulliken charge [e]. q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. DISTDistance from Ligand [Å]. TotalIFIE at MP2 level [kcal/mol]. ESElectro static interaction energy by PIEDA [kcal/mol]. EXExchange-repulsion energy by PIEDA [kcal/mol]. CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. DI(MP2)Dispersion energy by PIEDA [kcal/mol]. q(I=>J)Charge transfer value from I to J fragmens [e].
3A3VAL00.000-0.0103.3030.5152.3990.005-0.669-1.2200.000
4A4HIS0-0.0160.0075.230-0.400-0.322-0.001-0.007-0.0700.000
5A5ALA00.027-0.0108.8990.1100.1100.0000.0000.0000.000
6A6ALA0-0.002-0.00510.5720.0070.0070.0000.0000.0000.000
7A7ASP-1-0.904-0.94312.4330.1550.1550.0000.0000.0000.000
8A8GLN0-0.082-0.04211.7580.0200.0200.0000.0000.0000.000
9A9TYR0-0.015-0.0088.3090.0570.0570.0000.0000.0000.000
10A10LEU0-0.007-0.0042.856-1.455-0.7471.899-0.571-2.0360.002
11A11VAL00.0140.0134.148-0.2600.030-0.001-0.072-0.2170.000
12A12ALA00.0250.0052.434-3.330-1.8344.275-2.417-3.354-0.020
13A13PRO00.0730.0322.510-0.994-0.4720.7680.090-1.3800.000
14A14GLY0-0.031-0.0205.5390.1810.1810.0000.0000.0000.000
15A15GLU-1-0.898-0.9437.774-0.741-0.7410.0000.0000.0000.000
16A16ALA0-0.0020.0272.447-0.502-0.1340.638-0.256-0.7510.000
17A17ASP-1-0.803-0.9044.441-0.0020.108-0.001-0.008-0.1020.000
18A18LEU0-0.037-0.0324.113-0.486-0.3580.000-0.033-0.0950.000
19A19LEU0-0.002-0.0245.9480.4270.4270.0000.0000.0000.000
20A20GLU-1-0.873-0.9222.070-7.174-6.0113.791-2.043-2.912-0.025
21A21VAL0-0.019-0.0182.342-1.222-0.3194.618-1.735-3.785-0.001
22A22HIS0-0.049-0.0382.9703.0972.0590.0751.371-0.409-0.001
23A23ALA0-0.017-0.0046.0300.1770.1770.0000.0000.0000.000
24A24ARG10.8760.9412.330-5.950-6.5227.889-2.047-5.2700.012
25A25LEU00.0020.0035.161-0.649-0.507-0.001-0.034-0.1070.000
26A26ALA00.0060.0327.371-0.649-0.6490.0000.0000.0000.000
27A27GLY0-0.009-0.00610.480-0.037-0.0370.0000.0000.0000.000
28A28THR0-0.026-0.0358.769-0.140-0.1400.0000.0000.0000.000
29A29GLY0-0.067-0.02612.160-0.129-0.1290.0000.0000.0000.000
30A30LEU0-0.025-0.01210.309-0.150-0.1500.0000.0000.0000.000
31A31PHE0-0.0040.00010.5020.1960.1960.0000.0000.0000.000
32A32PRO00.0570.0417.557-0.052-0.0520.0000.0000.0000.000
33A33PRO0-0.035-0.0209.665-0.258-0.2580.0000.0000.0000.000
34A34PHE00.018-0.0265.997-0.126-0.1260.0000.0000.0000.000
35A35PRO00.0380.03611.2940.1270.1270.0000.0000.0000.000
36A36PRO0-0.0080.00710.7420.0110.0110.0000.0000.0000.000
37A37VAL0-0.001-0.01711.470-0.083-0.0830.0000.0000.0000.000
38A38GLU-1-0.767-0.8708.215-0.200-0.2000.0000.0000.0000.000
39A39LEU0-0.001-0.01311.1620.0120.0120.0000.0000.0000.000
40A40PRO00.0320.01211.842-0.049-0.0490.0000.0000.0000.000
41A41GLY0-0.008-0.01112.6390.0570.0570.0000.0000.0000.000
42A42GLY00.0960.0808.386-0.033-0.0330.0000.0000.0000.000
43A43VAL00.012-0.0125.5780.2030.2030.0000.0000.0000.000
44A44GLY00.010-0.0018.3090.0700.0700.0000.0000.0000.000
45A45GLY0-0.027-0.01210.7240.0280.0280.0000.0000.0000.000
46A46LEU0-0.0170.00410.2120.0150.0150.0000.0000.0000.000
47A47VAL00.008-0.00311.1480.0110.0110.0000.0000.0000.000
48A48ALA0-0.008-0.00513.886-0.020-0.0200.0000.0000.0000.000
49A49ARG10.9100.97113.300-0.079-0.0790.0000.0000.0000.000
50A50GLY00.0080.00216.947-0.004-0.0040.0000.0000.0000.000
51A51GLY0-0.035-0.00914.8800.0180.0180.0000.0000.0000.000
52A52PHE00.017-0.00414.379-0.054-0.0540.0000.0000.0000.000
53A53ALA00.013-0.00316.0640.0560.0560.0000.0000.0000.000
54A54GLN0-0.0410.00017.5920.0210.0210.0000.0000.0000.000
55A55THR0-0.014-0.01819.123-0.030-0.0300.0000.0000.0000.000
56A56PHE0-0.063-0.02315.922-0.021-0.0210.0000.0000.0000.000
57A57PHE00.033-0.00821.1750.0000.0000.0000.0000.0000.000
58A58PHE00.0490.02313.0410.0020.0020.0000.0000.0000.000
59A59PRO00.0510.02016.7820.0420.0420.0000.0000.0000.000
60A60ALA0-0.0150.01317.122-0.001-0.0010.0000.0000.0000.000
61A61GLU-1-0.775-0.84214.0150.5520.5520.0000.0000.0000.000
62A62VAL00.0040.01612.0310.1280.1280.0000.0000.0000.000
63A63LEU0-0.009-0.01111.438-0.100-0.1000.0000.0000.0000.000
64A64GLY00.026-0.00412.036-0.090-0.0900.0000.0000.0000.000
65A65LEU0-0.0190.02211.2030.0900.0900.0000.0000.0000.000
66A66THR00.0120.01111.345-0.043-0.0430.0000.0000.0000.000
67A67PHE00.0240.02412.549-0.021-0.0210.0000.0000.0000.000
68A68ARG10.9680.99915.2080.2230.2230.0000.0000.0000.000
69A69THR0-0.016-0.02517.5420.0090.0090.0000.0000.0000.000
70A70PRO00.0500.00921.080-0.019-0.0190.0000.0000.0000.000
71A71LYS10.8320.90423.5480.0740.0740.0000.0000.0000.000
72A72GLY00.0050.01421.9650.0000.0000.0000.0000.0000.000
73A73ARG10.8760.94621.1340.0890.0890.0000.0000.0000.000
74A74ARG10.8760.91913.7790.3710.3710.0000.0000.0000.000
75A75VAL0-0.029-0.01117.4400.0070.0070.0000.0000.0000.000
76A76ARG10.8760.9309.9770.3110.3110.0000.0000.0000.000
77A77ALA0-0.014-0.01615.1250.0150.0150.0000.0000.0000.000
78A78GLY0-0.019-0.01914.9530.0150.0150.0000.0000.0000.000
79A79GLY00.022-0.00413.743-0.042-0.0420.0000.0000.0000.000
80A80VAL0-0.015-0.01912.957-0.012-0.0120.0000.0000.0000.000
81A81VAL0-0.0090.01015.779-0.021-0.0210.0000.0000.0000.000
82A82VAL00.0550.03417.730-0.018-0.0180.0000.0000.0000.000
83A83LYS10.9250.97317.691-0.059-0.0590.0000.0000.0000.000
84A84ASN0-0.030-0.02219.456-0.015-0.0150.0000.0000.0000.000
85A85VAL00.0400.02223.1930.0110.0110.0000.0000.0000.000
86A86GLN0-0.056-0.02823.147-0.005-0.0050.0000.0000.0000.000
87A87GLY00.0830.04024.1330.0050.0050.0000.0000.0000.000
88A88TYR0-0.033-0.01824.282-0.004-0.0040.0000.0000.0000.000
89A89ASP-1-0.776-0.86720.4730.1180.1180.0000.0000.0000.000
90A90LEU00.024-0.00220.1180.0040.0040.0000.0000.0000.000
91A91VAL0-0.0200.00315.486-0.011-0.0110.0000.0000.0000.000
92A92ARG10.7930.85017.017-0.190-0.1900.0000.0000.0000.000
93A93LEU0-0.0470.00720.110-0.005-0.0050.0000.0000.0000.000
94A94PHE0-0.007-0.00215.258-0.007-0.0070.0000.0000.0000.000
95A95VAL0-0.0060.00115.6200.0020.0020.0000.0000.0000.000
96A96GLY00.0250.01518.031-0.005-0.0050.0000.0000.0000.000
97A97SER0-0.088-0.04619.568-0.025-0.0250.0000.0000.0000.000
98A98PHE00.004-0.02719.643-0.019-0.0190.0000.0000.0000.000
99A99GLY00.0240.02919.131-0.015-0.0150.0000.0000.0000.000
100A100LEU0-0.039-0.00419.992-0.020-0.0200.0000.0000.0000.000
101A101LEU00.014-0.00921.148-0.009-0.0090.0000.0000.0000.000
102A102GLY0-0.026-0.01519.555-0.014-0.0140.0000.0000.0000.000
103A103ARG10.8810.92611.1440.5330.5330.0000.0000.0000.000
104A104ALA00.0040.00511.751-0.022-0.0220.0000.0000.0000.000
105A105GLU-1-0.837-0.91610.908-0.450-0.4500.0000.0000.0000.000
106A106GLU-1-0.829-0.8976.274-0.692-0.6920.0000.0000.0000.000
107A107VAL0-0.002-0.0056.8340.0180.0180.0000.0000.0000.000
108A108VAL00.0080.0076.6080.1690.1690.0000.0000.0000.000
109A109LEU0-0.019-0.0127.542-0.144-0.1440.0000.0000.0000.000
110A110ARG10.9410.9599.051-0.384-0.3840.0000.0000.0000.000
111A111LEU0-0.0180.0067.3190.1280.1280.0000.0000.0000.000
112A112ARG10.7650.84611.406-0.751-0.7510.0000.0000.0000.000
113A113PRO00.0420.02314.0050.0860.0860.0000.0000.0000.000
114A114GLY0-0.034-0.02616.093-0.061-0.0610.0000.0000.0000.000
115A115ARG10.9080.95116.958-0.471-0.4710.0000.0000.0000.000
116A116ALA00.0340.03019.310-0.031-0.0310.0000.0000.0000.000
117A117GLN00.0510.02714.1680.0450.0450.0000.0000.0000.000
118A118ALA00.0190.00218.826-0.035-0.0350.0000.0000.0000.000
119A119PHE0-0.0310.00316.0870.0280.0280.0000.0000.0000.000
120A120LEU00.0140.02719.294-0.015-0.0150.0000.0000.0000.000
121A121ARG10.7990.89422.428-0.116-0.1160.0000.0000.0000.000
122A122ARG10.8960.94624.611-0.151-0.1510.0000.0000.0000.000
123A123PRO00.0690.04128.1250.0020.0020.0000.0000.0000.000
124A124PHE0-0.033-0.00928.5130.0040.0040.0000.0000.0000.000
125A125SER00.0260.00430.317-0.005-0.0050.0000.0000.0000.000
126A126GLY00.0260.01232.177-0.007-0.0070.0000.0000.0000.000
127A127SER0-0.054-0.02631.952-0.001-0.0010.0000.0000.0000.000
128A128PHE0-0.009-0.00225.2200.0050.0050.0000.0000.0000.000
129A129PRO00.0060.01728.681-0.004-0.0040.0000.0000.0000.000
130A130ARG10.9510.96929.555-0.135-0.1350.0000.0000.0000.000
131A131LEU0-0.014-0.00126.754-0.005-0.0050.0000.0000.0000.000
132A132VAL0-0.0230.00829.7420.0060.0060.0000.0000.0000.000
133A133PRO00.0370.00326.941-0.008-0.0080.0000.0000.0000.000
134A134THR00.0300.00325.128-0.004-0.0040.0000.0000.0000.000
135A135PRO0-0.0140.01621.7500.0180.0180.0000.0000.0000.000
136A136ARG10.8520.93917.943-0.493-0.4930.0000.0000.0000.000
137A137PHE0-0.006-0.01714.3940.0200.0200.0000.0000.0000.000
138A138LEU0-0.005-0.01019.205-0.012-0.0120.0000.0000.0000.000
139A139PHE0-0.027-0.01717.6860.0010.0010.0000.0000.0000.000
140A140ALA00.0300.02122.1190.0030.0030.0000.0000.0000.000
141A141LEU0-0.027-0.02620.160-0.002-0.0020.0000.0000.0000.000
142A142GLU-1-0.863-0.93023.8620.0620.0620.0000.0000.0000.000
143A143ASP-1-0.892-0.93924.1580.0860.0860.0000.0000.0000.000
144A144GLU-1-0.928-0.97227.0290.0310.0310.0000.0000.0000.000
145A145GLU-1-0.897-0.94528.5380.0870.0870.0000.0000.0000.000
146A146GLY00.0590.03329.904-0.002-0.0020.0000.0000.0000.000
147A147PRO0-0.038-0.01728.2150.0050.0050.0000.0000.0000.000
148A148TRP00.0130.00925.4190.0100.0100.0000.0000.0000.000
149A149LEU0-0.043-0.03025.3550.0030.0030.0000.0000.0000.000
150A150TYR00.030-0.00120.3820.0090.0090.0000.0000.0000.000
151A151ALA0-0.003-0.00521.3140.0030.0030.0000.0000.0000.000
152A152TYR0-0.033-0.02313.4780.0380.0380.0000.0000.0000.000
153A153HIS00.0250.00418.6550.0320.0320.0000.0000.0000.000
154A154PHE00.0470.01815.0530.0180.0180.0000.0000.0000.000
155A155GLY00.0190.00718.668-0.024-0.0240.0000.0000.0000.000
156A156HIS00.0310.01320.2660.0230.0230.0000.0000.0000.000
157A157PRO00.0640.01523.108-0.008-0.0080.0000.0000.0000.000
158A158LYS10.9850.99624.640-0.187-0.1870.0000.0000.0000.000
159A159GLU-1-0.951-0.97524.5780.2260.2260.0000.0000.0000.000
160A160VAL0-0.061-0.03521.191-0.009-0.0090.0000.0000.0000.000
161A161GLU-1-0.893-0.93724.3780.2120.2120.0000.0000.0000.000
162A162ARG10.9580.97527.470-0.195-0.1950.0000.0000.0000.000
163A163PHE0-0.040-0.01723.314-0.008-0.0080.0000.0000.0000.000
164A164ARG10.8520.89221.477-0.298-0.2980.0000.0000.0000.000
165A165GLU-1-0.954-0.96027.2840.1380.1380.0000.0000.0000.000
166A166ALA0-0.032-0.00730.155-0.011-0.0110.0000.0000.0000.000
167A167PHE0-0.092-0.04925.644-0.009-0.0090.0000.0000.0000.000
168A168GLY00.0690.05129.057-0.012-0.0120.0000.0000.0000.000
169A169GLY0-0.042-0.03428.1070.0110.0110.0000.0000.0000.000
170A170GLU-1-0.837-0.89725.7200.1280.1280.0000.0000.0000.000
171A171GLU-1-0.802-0.89921.4860.2990.2990.0000.0000.0000.000
172A172ALA00.0050.00620.280-0.019-0.0190.0000.0000.0000.000
173A173ARG10.9460.95717.686-0.125-0.1250.0000.0000.0000.000
174A174PRO0-0.005-0.01512.485-0.012-0.0120.0000.0000.0000.000
175A175LEU0-0.0120.01514.364-0.042-0.0420.0000.0000.0000.000
176A176ASP-1-0.762-0.86813.490-0.100-0.1000.0000.0000.0000.000
177A177LEU00.010-0.01014.616-0.007-0.0070.0000.0000.0000.000
178A178ARG10.7930.87110.0480.3220.3220.0000.0000.0000.000
179A179PRO0-0.005-0.00916.206-0.003-0.0030.0000.0000.0000.000
180A180ARG10.8370.90519.366-0.046-0.0460.0000.0000.0000.000
181A181PHE0-0.068-0.02518.5880.0120.0120.0000.0000.0000.000
182A182PRO00.0520.03419.313-0.016-0.0160.0000.0000.0000.000
183A183ARG10.8040.88820.6660.0170.0170.0000.0000.0000.000
184A184GLY0-0.0040.00118.801-0.003-0.0030.0000.0000.0000.000
185A185LEU0-0.039-0.02916.4960.0120.0120.0000.0000.0000.000
186A186GLY00.0080.02119.4570.0090.0090.0000.0000.0000.000
187A187LEU0-0.048-0.03522.6000.0140.0140.0000.0000.0000.000
188A188GLY00.016-0.01225.305-0.011-0.0110.0000.0000.0000.000
189A189GLU-1-0.910-0.94227.7300.0450.0450.0000.0000.0000.000
190A190GLY00.000-0.00926.105-0.005-0.0050.0000.0000.0000.000
191A191PRO00.001-0.00223.8420.0060.0060.0000.0000.0000.000
192A192LEU00.0010.01518.5370.0100.0100.0000.0000.0000.000
193A193TRP0-0.0150.00223.204-0.008-0.0080.0000.0000.0000.000
194A194ASP-1-0.758-0.85319.9510.1980.1980.0000.0000.0000.000
195A195LEU0-0.032-0.02422.979-0.014-0.0140.0000.0000.0000.000
196A196ARG10.7880.90219.097-0.187-0.1870.0000.0000.0000.000
197A197PHE0-0.018-0.01221.391-0.017-0.0170.0000.0000.0000.000
198A198ARG10.9010.96424.211-0.044-0.0440.0000.0000.0000.000
199A199TYR0-0.064-0.07619.671-0.010-0.0100.0000.0000.0000.000
200A200GLN00.0120.00623.450-0.002-0.0020.0000.0000.0000.000
201A201ASP-1-0.732-0.84622.704-0.044-0.0440.0000.0000.0000.000
202A202GLY0-0.029-0.01522.9440.0000.0000.0000.0000.0000.000
203A203GLY0-0.0390.00224.4550.0000.0000.0000.0000.0000.000
204A204ALA00.0100.00325.114-0.007-0.0070.0000.0000.0000.000
205A205SER00.0420.01424.2220.0080.0080.0000.0000.0000.000
206A206PRO00.0010.00524.091-0.002-0.0020.0000.0000.0000.000
207A207PRO0-0.0030.00127.195-0.007-0.0070.0000.0000.0000.000
208A208PRO00.0120.00027.3610.0060.0060.0000.0000.0000.000
209A209PRO00.0380.03029.094-0.004-0.0040.0000.0000.0000.000
210A210PRO00.0750.00831.771-0.005-0.0050.0000.0000.0000.000
211A211ALA0-0.034-0.02232.120-0.005-0.0050.0000.0000.0000.000
212A212PHE00.0600.01024.054-0.006-0.0060.0000.0000.0000.000
213A213LEU00.0240.02228.808-0.008-0.0080.0000.0000.0000.000
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